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Steven R. Ness, Ph.D.

s n e s s AT s n e s s . n e t

Victoria, British Columbia, Canada

Zax Institute

sness.net LinkedIn Google Scholar Medium Github sness Github sness23 Sourceforge ResearchGate OpenReview ACM ScholarGPS IEEE AMiner

Summary

An interdisciplinary scientific programmer and computational biologist with a Ph.D. in Computer Science and over 30 years driving high‑impact research, product development, and AI‑powered biotech ventures. I combine deep domain expertise in structural biology and protein‑ligand docking with hands‑on machine‑learning and software‑engineering leadership.

Key Qualifications & Achievements

Founding AI‑Driven Biotech Platforms:

– Built and scaled folding.ai (2021–2025) and doi.bio (2025–Present), end‑to‑end intelligence‑augmentation systems that integrate generative models with GPU‑accelerated molecular viewers to triage and design novel therapeutics.

Enterprise ML & Infrastructure Leadership:

– As Lead Member of Technical Staff at Salesforce, designed and delivered production‑scale service‑mesh infrastructure (Envoy/Istio), voice‑AI assistants, and master‑data orchestration (Data Cloud) now serving millions of profiles.

Proven Scientific Programmer & Researcher:

– Authored CRANK (GPL‑licensed crystallography pipeline used by 100+ labs) and Gamma docking suite (University of Alberta), and published in Nature, Structure, and Biochemistry.

Cross‑Functional Collaboration & Wet‑Lab Integration:

– Partnered with protein designers and biologists throughout PhD (Orchive bioacoustic ML) and later roles to translate experimental feedback into model refinements, achieving high‑accuracy detection/classification and driving wet‑lab testing campaigns ([sness.net][1]).

Alignment with Latent Labs Responsibilities

Building ML Models for the Physical World :

I’ve rapidly prototyped generative and deep‑learning models—from orca‑call classification to AI‑driven protein design—and defined custom evaluation metrics tied directly to experimental success.

Data Curation & Metric Development:

The Orchive project involved curating 20 000+ hrs of audio to train ML pipelines and devising benchmark classification metrics; I’ve also managed large bioinformatics datasets and high‑throughput pipelines in genomics.

Collaborative Codebase & Infrastructure Maintenance:

I’ve led joint codebases with strict CI/CD, Docker/PM2 deployments, and cloud (AWS/GCP) architectures, ensuring robust, maintainable software across multi‑disciplinary teams.

Wet‑Lab Planning & Model Inference:

With hands‑on roles in structural biology labs (UBC, Leiden) and biotech startups, you’ve planned wet‑lab assays, performed in‑silico inference, and iteratively improved models based on real‑world feedback.

Continuous Learning & Knowledge Sharing:

I regularly publish at leading conferences (ICML, ISMIR), organize reading groups, and mentor across academia and industry, staying at the forefront of ML and cell‑biology advances.

💼 Professional Experience

Founder – doi.bio (Self‑employed)

Mar 2025 – Present (5 mo) · Victoria, BC (Hybrid)

Founder of doi.bio.

Founder & CEO – folding.ai

May 2021 – Mar 2025 (3 yr 11 mo) · Victoria, BC

Software Engineer – Quip

May 2020 – Apr 2021 (1 yr)

Lead Member Of Technical Staff, Einstein Voice Assistant – Salesforce Research

Nov 2019 – May 2020 (7 mo) · San Francisco, CA

Member of the Einstein Voice Assistant team (formerly MetaMind), building an AI‑based voice assistant smart‑speaker integrated with Salesforce core.

Lead Member Of Technical Staff, Service Mesh – Salesforce

Nov 2018 – Nov 2019 (1 yr 1 mo) · San Francisco, CA

Delivered Envoy proxy implementation and collaborated with Istio to deploy service‑mesh infrastructure for Salesforce Hyperforce / Customer 360.

Lead Member Of Technical Staff, Team Lead – Customer 360 – Salesforce

Feb 2016 – Nov 2018 (2 yr 10 mo) · San Francisco, CA

Founding member and UI Team Lead of the Customer 360 tiger team; presented demos to Salesforce founders and EVPs; partnered with architects to deliver the Customer 360 Data Manager product.

Senior Software Developer – Priologic Software Inc.

Oct 2013 – Oct 2014 (1 yr 1 mo) · Victoria, BC

Developed EasyRTC (open‑source WebRTC server/client SDKs) for web, iOS, and Android (GitHub).

Ph.D. Student

University of Victoria (Jan 2010 – Dec 2013 | 4 yrs) Victoria, BC

Projects:

Orchive – Data mining a massive bioacoustic archive of 20 000+ hrs of orca recordings from OrcaLab (1980 – present), with a web-based interface for researchers.

Cantillion – Designed and implemented the Cantillion interface (uploaded Oct 16, 2013).

• Cal500 – Music annotation dataset development.

Ocean Networks Canada (VENUS/NEPTUNE) – Sensor data integration and analysis.

M.Sc. Student

University of Victoria (2007 – Dec 2009 | 3 yrs) Victoria, BC

Projects:

Orchive – Early prototyping of the bioacoustic archive interface.

Cantillion – Initial interface design and implementation.

Audioscapes – Exploratory work on large-scale music analysis.

Software Engineering Intern

Google (News Performance Team)

May 2012 – Aug 2012 (4 mos)

• Reduced end‑to‑end latency in Google News by ~33% for users on slow connections.

• Developed a JavaScript API for real‑time performance monitoring.

• Identified critical bottlenecks, implemented fixes, and deployed to production.

Software Research Intern

Google Research (Human Auditory Models)

May 2011 – Aug 2011 (4 mos)

May 2010 – Aug 2010 (4 mos)

• Built electronic models of the human auditory system to analyze large-scale music data.

• Wrote data‑processing pipelines and ran experiments over thousands of YouTube music videos using Google’s compute infrastructure.

Scientific Programmer

Leiden University

Sep 2003 – Jan 2006 (2 yrs 5 mos)

• Designed and implemented Crank, an open‑source platform for automated crystallographic structure solution (Tcl, C, Shell, Fortran).

• “Crank” is GPL‑licensed and used by 100+ labs as part of CCP4.

Senior Programmer

BC Genome Sciences Centre

Feb 2000 – Sep 2001 (1 yr 8 mos)

• Developed software for constructing and analyzing physical maps of large genomes.

• Coordinated complete restriction‑map efforts for mouse, rat, and cow genomes.

• Enhanced the industry‑standard FPC platform with new features.

• Trained programmers and genomics technicians; designed custom fingerprint‑analysis tools.

Programmer

Stormix Technologies Inc.

Sep 1999 – Jan 2000 (5 mos)

• Kernel‑level and hardware‑detection programming for Storm Linux 2000.

• Implemented boot‑time splash screen with PC‑speaker audio.

• Developed nanoGUI, a graphics library for embedded devices.

Structural Biochemist Researcher & Software Engineer / Systems Administrator

University of British Columbia

May 1997 – Sep 1999 (2 yrs 5 mos)

• Managed 10 SGI/Linux lab workstations, user accounts, and network services (Apache, sendmail, Samba, NFS).

• Developed and maintained an extensive HTML crystallography reference library.

• Provided UNIX training for beginners.

• Languages/Tools: C, C++, Fortran 77, Bash, C shell, Perl, IRIX.

Software Developer in Structural Biochemistry

University of Alberta

Jan 1995 – Apr 1997 (2 yrs 4 mos)

• Created Gamma, a molecular‑docking program using genetic‑algorithm optimization.

• Built GUIs for Research, RSDataBase, and Gamma command‑line tools.

• Implemented a 3D molecular viewer with SGI Open Inventor.

• Languages: C, C++, Fortran 77, Bash, C shell.

Structural Biochemistry Software Developer Intern

University of Alberta

Sep 1992 – May 1995 (2 yrs 9 mos)

• Designed a general‑purpose genetic‑algorithm optimizer.

• Developed clustering software for analyzing docking results.

• Language: C, C++.

Programmer Intern

Alberta Environment Research Centre

Jul 1987 – Aug 1987 (2 mos)

• Developed timekeeping and scheduling software with database integration.

• Language: Turbo Pascal.

Education

• Ph.D., Computer Science

University of Victoria

2010 – 2013 · GPA: 9.0

• M.Sc., Computer Science

University of Victoria

2007 – 2010 · GPA: 9.0

Activities: Computer Science Course Union (community teaching), Society for Indian Classical Music

Volunteering

President — Society for Indian Classical Arts, University of Victoria

Jan 2010 – Dec 2013 (4 yr) · Arts & Culture

Lead Developer & Scientist — The Orchive

May 2007 – Jan 2025 (17 yr 9 mo) · Animal Welfare

Developed and maintained the Orchive website (23 000+ hours of orca vocalizations; bioacoustic archive annotation tools).

CORE COMPETENCIES

• Programming / DevOps: Python, Java, C/C++, C#, JavaScript; Linux, Git, Docker, PM2, CI/CD([ResearchGate][1])
• AI / Data Science: classical & deep learning, LSH, signal processing, recommender systems
• Structural Biology: macromolecular crystallography, docking, structure‑based drug design
• Bioinformatics & Genomics: physical/sequence mapping, variant annotation, high‑throughput pipelines
• Cloud & Distributed Systems: AWS & GCP services, event‑stream architectures, Salesforce Data Cloud
• Leadership: project & product ownership, grant writing, mentoring, university teaching

Publications

Full list: Google Scholar.

Integrated entity view across distributed systems

US Patent 10,936,582

ORCA-SLANG: An Automatic Multi-Stage Semi-Supervised Deep Learning Framework for Large-Scale Killer Whale Call Type Identification.

C Bergler, M Schmitt, AK Maier, H Symonds, P Spong, SR Ness, …

Interspeech, 2396-2400

User interface for commerce architecture

D Woodward, A Chadda, D Hacker, N Steven, M Lagrotte, J Moody, C Bill, …

US Patent App. 16/264,391

Orchive

S Ness

Human and machine annotation in the Orchive, a large scale bioacoustic archive

S Ness, G Tzanetakis

2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP …

Taking a walk on the wild side: teaching cloud computing on distributed research testbeds

Y Zhuang, C Matthews, S Tredger, S Ness, J Short-Gershman, L Ji, …

Proceedings of the 45th ACM technical symposium on Computer science …

The Orchive: Data mining a massive bioacoustic archive

S Ness, H Symonds, P Spong, G Tzanetakis

arXiv preprint arXiv:1307.0589

The Orchive: A system for semi-automatic annotation and analysis of a large collection of bioacoustic recordings

S Ness

University of Victoria (Canada)

Sonophenology: A multimodal tangible interface for the sonification of phenological data at multiple time-scales

S Ness, P Reimer, J Love, WA Schloss, G Tzanetakis

Journal on Multimodal User Interfaces 5 (3), 123-129

On Computational Transcription and Analysis of Candences in Oral and Semi-Oral Chant Traditions

D Biro, P Van Kranenburg, S Ness, G Tzanetakis, A Volk

Proceedings of the Second International Conference on Analytical Approaches …

On computational transcription and analysis of oral and semi-oral chant traditions

DP Biró, P Van Kranenburg, SR Ness, G Tzanetakis, A Volk

Proceedings of the Analytical Approaches to World Music Conference, AAWM 2012

Stability and variation in cadence formulas in oral and semi-oral chant traditions–a computational approach

DP Biró, P van Kranenburg, SR Ness, G Tzanetakis, A Volk

Proceedings of the 12th International Conference on Music Perception and …

Auditory sparse coding

SR Ness, T Walters, RF Lyon

Music Data Mining. Boca Raton, FL, 33487-2742

Strategies for orca call retrieval to support collaborative annotation of a large archive

SR Ness, A Lerch, G Tzanetakis

2011 IEEE 13th International Workshop on Multimedia Signal Processing, 1-6

Music Information Robotics: Coping Strategies for Musically Challenged Robots.

SR Ness, S Trail, PF Driessen, WA Schloss, G Tzanetakis

ISMIR, 567-572

Automatic event detection for long-term monitoring of hydrophone data

F Sattar, PF Driessen, G Tzanetakis, SR Ness, WH Page

Proceedings of 2011 IEEE Pacific Rim Conference on Communications, Computers …

Controlling Real time sound spatialization using the radiodrum

SR Ness, G Odowichuk, PF Driessen, G Tzanetakis

ICMC 2011

A computational investigation of melodic contour stability in Jewish Torah Trope Performance Traditions

P Van Kranenburg, DP Biró, SR Ness, G Tzanetakis

Proceedings of the International Society on Music Information Retrieval …

Gesture Analysis of Radiodrum Data

SR Ness, S Methabi, G Odowichuk, G Tzanetakis, WA Schloss

ICMC 2011

Computer-assisted cantillation and chant research using content-aware web visualization tools

SR Ness, DP Biró, G Tzanetakis

Multimedia Tools and Applications 48 (1), 207-224

Sonophenology: a tangible interface for sonification of geo-spatial phenological data at multiple time-scales

SR Ness, P Reimer, N Krell, G Odowichuck, WA Schloss, G Tzanetakis

Geoshuffle: Location-Aware, Content-based Music Browsing Using Self-organizing Tag Clouds.

S Miller, P Reimer, SR Ness, G Tzanetakis

ISMIR, 237-242

Improving automatic music tag annotation using stacked generalization of probabilistic svm outputs

SR Ness, A Theocharis, G Tzanetakis, LG Martins

Proceedings of the 17th ACM international conference on Multimedia, 705-708

Assistive music browsing using self-organizing maps

G Tzanetakis, MS Benning, SR Ness, D Minifie, N Livingston

Proceedings of the 2nd International Conference on PErvasive Technologies …

Content-aware web browsing and visualization tools for cantillation and chant research

SR Ness, G Tzanetakis, DP Biró

2009 Seventh International Workshop on Content-Based Multimedia Indexing, 81-86

Assistive music browsing using self-organizing maps

S Ness

Proceedings of the 2nd International Conference on PErvsive Technologies …

New tools for use in the musicology of record production

K McNally, G Tzanetakis, SR Ness

Content-aware visualizations of audio data in diverse contexts

S Ness

MIREX 2010

S Ness, G Tzanetakis

### Somba: multiuser music creation using self-organizing maps and motion tracking

SR Ness, G Tzanetakis

ICMC

Audioscapes: exploring surface interfaces for music exploration

SR Ness, G Tzanetakis

ICMC

Chants and orcas: semi-automatic tools for audio annotation and analysis in niche dom

ains

SR Ness, M Wright, LG Martins, G Tzanetakis

Proceedings of the 2nd ACM workshop on Multimedia semantics, 9-16

Decoding the song: Histogram-based paradigmatic and syntagmatic analysis of melodic formulae in Hungarian laments, Torah trope, tenth century plainchant and Koran recitation

DP Biró, S Ness, WA Schloss, G Tzanetakis, M Wright

Phase refinement through density modification

JP Abrahams, JR Plaisier, S Ness, NS Pannu

Macromolecular Crystallography: conventional and high-throughput methods, 143

Extending the resolution and phase-quality limits in automated model building with iterative refinement

P Skubák, S Ness, NS Pannu

Biological Crystallography 61 (12), 1626-1635

Crank-New Methods in Automated Structure Solution

SR Ness, RAG de Graaff, JP Abrahams, NS Pannu

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 61, C55-C55, 2005

CRANK: new methods for automated macromolecular crystal structure solution

SR Ness, RAG de Graaff, JP Abrahams, NS Pannu

Structure 12 (10), 1753-1761, 2005

CRANK-new methods for automated structure solution

S Ness, RAG de Graaff, JP Abrahams, NS Pannu

Foundations of Crystallography 60 (a1), s16-s16, 2004

A physical map of the mouse genome

SG Gregory, M Sekhon, J Schein, S Zhao, K Osoegawa, CE Scott, …

Nature 418 (6899), 743-750

Assembly of fingerprint contigs: parallelized FPC

SR Ness, W Terpstra, M Krzywinski, MA Marra, SJM Jones

Bioinformatics 18 (3), 484-485

Structural models for the alkaline conformers of yeast iso‐1‐ferricytochrome c

SR Ness, TP Lo, AG Mauk

Israel Journal of Chemistry 40 (1), 21-25

Structure-Based Design Guides the Improved Efficacy of Deacylation Transition State Analogue Inhibitors of TEM-1 β-Lactamase,

S Ness, R Martin, AM Kindler, M Paetzel, M Gold, SE Jensen, JB Jones, …

Biochemistry 39 (18), 5312-5321

Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment

TN Hart, RE Gillilan, R Lilien, SR Ness, RJ Read

High Performance Computing Systems and Applications, 309-322

Critical evaluation of the research docking program for the CASP2 challenge

TN Hart, SR Ness, RJ Read

Proteins: Structure, Function, and Bioinformatics 29 (S1), 205-209

GAMMA: a new docking program utilizing an advanced evolution system algorithm as an engine

S Ness, T Hart, R Read

Acta Crystallographica Section A 52, C90-C90, 1996

Monte Carlo algorithms for docking to proteins

RJ Read, TN Hart, MD Cummings, SR Ness

Supramolecular Chemistry 6 (1-2), 135-140

PATENTS

• Integrated Entity View Across Distributed Systems, US 10 936 582 B2 (2021) – master‑data federation.([Google Patents][4])

• User Interface for Commerce Architecture, US 11 442 952 B2 (2023) – low‑code composable storefront UI.([Google Patents][5])

SELECT AWARDS & HONOURS

• National Science Fair Best Senior Project + Multiple Gold Medallist (Canada) – Secondary School

• NSERC CGS‑D Doctoral Scholarship, University of Victoria

• Salesforce CTO Award (New Customer Experience)

COMMUNITY & LEADERSHIP

• Mentor, How to Grow Almost Anything (MIT Media Lab / Ginkgo Bioworks joint course) – guiding student wet‑lab projects (2025).

• Speaker, ICML Workshop, ISMIR, CCP4 Study Weekend, Dockvision

LANGUAGES

English (native) - French (basic) • Dutch (basic) - Mandarin (basic)